Geological carbon sequestration in basalts is a promising solution to mitigate carbon emissions into the Earth's atmosphere. The Wallula pilot well in Eastern Washington State, USA provides an opportunity to investigate how native microbial communities in basalts are affected by the injection of supercritical carbon dioxide into deep, alkaline formation waters of the Columbia River Basalt Group. Our objective was to characterize the microbial communities at five depth intervals in the Wallula pilot well prior to CO2 injection to establish a baseline community for comparison after the CO2 is injected. Microbial communities were examined using quantitative polymerase chain reaction to enumerate bacterial cells and 454 pyrosequencing to compare and contrast the diversity of the native microbial communities. The deepest depth sampled contained the greatest amount of bacterial biomass, as well as the highest bacterial diversity. The shallowest depth sampled harbored the greatest archaeal diversity. Pyrosequencing revealed the well to be dominated by the Proteobacteria, Firmicutes, and Actinobacteria, with microorganisms related to hydrogen oxidizers (Hydrogenophaga), methylotrophs (Methylotenera), methanotrophs (Methylomonas), iron reducers (Geoalkalibacter), sulfur oxidizers (Thiovirga), and methanogens (Methermicocccus). Thus, the Wallula pilot well is composed of a unique microbial community in which hydrogen and single-carbon compounds may play a significant role in sustaining the deep biosphere.